File Changes for kent

v357_base to v358_preview (2017-10-30 to 2017-11-06) v358

• src/hca/LICENSE
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    7fb8f954d43e80d0ac739601d017df814e3d0aff Thu Aug 3 12:27:05 2017 -0700
    Updating copyright holder per HCA request.
• src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c
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    54233e68e0cb7825f81de963011e83849e128f38 Thu Sep 7 15:30:13 2017 -0700
    Adapting to some changed tag names.
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/hcaV2ToV3/2to3
  • lines changed 134, context: html, text, full: html, text
    f3256f82f0a5eb915068c65290675b315ee20678 Fri Sep 1 14:02:27 2017 -0700
    Adding table that describes how v2 metadata fields move to v3.
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    31139fbd0ac42c06d02e2d534831d719de4b5a0d Fri Sep 1 15:51:19 2017 -0700
    Renaming stuff for going between metadata versions.
• src/hca/toHca/hcaAddUuidToStorm/hcaAddUuidToStorm.c
  • lines changed 106, context: html, text, full: html, text
    050e1358247ac10835441952c2e192613f07f834 Thu Sep 7 16:51:12 2017 -0700
    Starting to add ids if missing for protocols and donors. Protocol bits might still need some work.
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c
  • lines changed 103, context: html, text, full: html, text
    822de6b51fb45bd9cea5f8c0e6e463f018e55db0 Thu Sep 7 13:20:48 2017 -0700
    Updating files[] array to lanes[] array as part of V2 -> V3 transition.
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    46ab8cdb3b6354c753c458ffba1a31a7f3bcae9b Thu Sep 7 15:18:58 2017 -0700
    Handling .1. .2. .3. output as arrays.
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    7e67a21cf569cafee3228bf6452e2e760ca7365f Thu Sep 7 15:31:01 2017 -0700
    Ooops, 'lanes' not lane.
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    233236f4f7c048d8be8cf861d047909b10e2af5a Thu Sep 7 21:43:00 2017 -0700
    Removing old V2 protocol handling. V3 doesn't need the special case.
  • lines changed 148, context: html, text, full: html, text
    40c64e7dd6319e8bba943fdfea4608e53b13ac27 Fri Sep 8 18:28:58 2017 -0700
    Removing debugging message
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    2ccd1bd9cee67dc597157a6e47d2694b93c954e6 Fri Sep 8 19:12:17 2017 -0700
    Handling another fringe case of dots in a characteristics name.
  • lines changed 14, context: html, text, full: html, text
    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/v2_v3/2to3
  • lines changed 134, context: html, text, full: html, text
    31139fbd0ac42c06d02e2d534831d719de4b5a0d Fri Sep 1 15:51:19 2017 -0700
    Renaming stuff for going between metadata versions.
  • lines changed 134, context: html, text, full: html, text
    1c61e4ebd646d8f13315dedb80affecdf9f5048e Fri Sep 1 15:51:40 2017 -0700
    Renaming stuff for going between metadata versions.
• src/hca/v2v3/2to3
  • lines changed 134, context: html, text, full: html, text
    1c61e4ebd646d8f13315dedb80affecdf9f5048e Fri Sep 1 15:51:40 2017 -0700
    Renaming stuff for going between metadata versions.
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    6f2a2d9ff2a77477878405e84f84777a04d57615 Mon Sep 4 11:56:48 2017 -0700
    Figuring out ways to modify a few less and fixing a few ontology terms.
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    442874e2a5188ef0ca1da03d42c367727f98c372 Wed Sep 6 17:21:09 2017 -0700
    Fixing a few typos and missing things.
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    56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700
    Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
• src/hca/v2v3/hcav2v3ArraysToMidObject/hcav2v3ArraysToMidObject.c
  • lines changed 83, context: html, text, full: html, text
    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
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    859c57e6d9c604e8c085f8a5c982f0f291a07ecf Sun Sep 3 11:35:58 2017 -0700
    Adding a bunch more things that are now arrays of objects.
• src/hca/v2v3/hcav2v3ArraysToMidObject/makefile
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    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
• src/hca/v2v3/hcav2v3ModifyContributors/hcav2v3ModifyContributors.c
  • lines changed 69, context: html, text, full: html, text
    a4861751824ae955f43dd60d321eb0c70620c19d Fri Sep 1 19:41:44 2017 -0700
    LIttle utility to fix up project.contributor in v2-v3 conversion seems to work.
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    7ce01a443f1fc128226f3d50455c55b5fb0b9bce Fri Sep 1 19:57:00 2017 -0700
    Unpacking more arrays.
  • lines changed 79, context: html, text, full: html, text
    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
• src/hca/v2v3/hcav2v3ModifyContributors/makefile
  • lines changed 3, context: html, text, full: html, text
    a4861751824ae955f43dd60d321eb0c70620c19d Fri Sep 1 19:41:44 2017 -0700
    LIttle utility to fix up project.contributor in v2-v3 conversion seems to work.
  • lines changed 3, context: html, text, full: html, text
    af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700
    Renaming conversion program that expanded in scope to indicate it's new scope.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 86, context: html, text, full: html, text
    30aecb6730202593ae34967fe4ce07647d9acdaa Mon Oct 30 11:29:38 2017 -0700
    Making pie charts have an 'other' slice that collects together the pieces that are really too small to label.
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    195a8f91ef9142b437a126f7a25634408f65f12c Wed Nov 1 15:24:20 2017 -0700
    Bumping cdwWebBrowse version number since it's changed a bit.
• src/hg/cirm/cdw/makefile
  • lines changed 1, context: html, text, full: html, text
    be508ea1e3d9043b295ee9b8826f89dc300a3851 Mon Sep 4 11:58:02 2017 -0700
    Using kentSrc define one more place to avoid future edits.
• src/hg/oneShot/freen/freen.c
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    018ef2c233c992fbbc573da09f9d7a01799828ad Tue Jul 18 16:45:54 2017 -0700
    Testing jsonWriteDouble();
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    de453283f2c66364b952d5e1745652fb37027008 Mon Sep 4 12:04:57 2017 -0700
    Testing some stuff for tagStorm array support.
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    ec4cc6c85b75e159916f9051de61e602c3cfc575 Tue Sep 5 12:33:28 2017 -0700
    Freen tests a function that is a little tricky used in building up tagStorm schemas involving arrays.
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    4929a9a5c8d7170a976fb2189f6dbee664be7790 Tue Sep 5 16:04:39 2017 -0700
    Testing some of the tag storm array processing stuff for tagStormCheck
• src/inc/tagSchema.h
  • lines changed 10, context: html, text, full: html, text
    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
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    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/inc/tagToSql.h
  • lines changed 1, context: html, text, full: html, text
    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
• src/lib/jsonWrite.c
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    165743602ab381693f1f340dd7c3693e6f662343 Tue Jul 18 16:46:34 2017 -0700
    Changing jsonWriteDouble printf format from %lf to %g for jsonWriteDouble.
• src/lib/tagSchema.c
  • lines changed 77, context: html, text, full: html, text
    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
  • lines changed 53, context: html, text, full: html, text
    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/lib/tagToJson.c
  • lines changed 9, context: html, text, full: html, text
    b16f8d69be2fe49227f2a1d72214228763bc53b6 Tue Jul 18 16:48:16 2017 -0700
    Making ttjMakeSubObj() handle null and empty prefix parameters.
• src/lib/tagToSql.c
  • lines changed 24, context: html, text, full: html, text
    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
  • lines changed 1, context: html, text, full: html, text
    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/tabFile/tabQuery/tabQuery.c
  • lines changed 1, context: html, text, full: html, text
    857a84306ccc2fc4f6147edd822d1153dba507da Mon Sep 4 12:08:25 2017 -0700
    Adding another verbose(2) level for debugging.
• src/tagStorm/tagSchemaToJson/tagSchemaToJson.c
  • lines changed 58, context: html, text, full: html, text
    f959d4aeea0c00a3116be9a62648a0d70a775fb8 Wed Sep 6 11:45:21 2017 -0700
    Adding shortcuts option
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    f42040eda7ad73e000510a0c3750f42b55a60c83 Wed Sep 6 12:24:54 2017 -0700
    Improving shortcut handling.
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    f3fb971b8bb28090c5d0f8a72f4063dde9e67280 Thu Sep 7 11:02:00 2017 -0700
    Making descriptions work better with subobjects, and arrays of subobjects work better.
• src/tagStorm/tagSchemaToJson/test.schema
  • lines changed 114, context: html, text, full: html, text
    aff5997f4c5ffa408b6be5de0a94a2bee8ccb2d6 Wed Sep 6 17:22:00 2017 -0700
    Updating test.schema to reflect HCA V3 more closely.
• src/tagStorm/tagStormCheck/tagStormCheck.c
  • lines changed 6, context: html, text, full: html, text
    4e1c6cfbdfa69c61a2a02be485297e786e0a0c9c Mon Sep 4 14:10:31 2017 -0700
    Adapting tagStormCheck for internal arrays.
  • lines changed 116, context: html, text, full: html, text
    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/tagStorm/tagStormCheck/test.schema
  • lines changed 5, context: html, text, full: html, text
    d931a2f62577733ea2db68a37d8e31bc2160edf6 Tue Sep 5 16:03:30 2017 -0700
    Updating test set for new functionality.
• src/tagStorm/tagStormCheck/test.tags
  • lines changed 14, context: html, text, full: html, text
    d931a2f62577733ea2db68a37d8e31bc2160edf6 Tue Sep 5 16:03:30 2017 -0700
    Updating test set for new functionality.
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 14, context: html, text, full: html, text
    252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700
    Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
  • lines changed 1, context: html, text, full: html, text
    984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700
    Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
• src/tagStorm/tagStormInfo/tests/expected.counts
  • lines changed 11, context: html, text, full: html, text
    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/expected.out
  • lines changed 4, context: html, text, full: html, text
    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/expected.schema
  • lines changed 11, context: html, text, full: html, text
    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/expected.vals
  • lines changed 33, context: html, text, full: html, text
    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/tagStorm/tagStormInfo/tests/test.in
  • lines changed 19, context: html, text, full: html, text
    2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700
    Updating test sets for new functionality.
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
  • lines changed 103, context: html, text, full: html, text
    6b6763ede646c2be8b8929c2a8700a4a68565cf1 Mon Jul 10 09:58:08 2017 -0700
    Creating a json output option.